Originally Posted by PanAm916
That's a long way to go on the A or C (or E depending on where you start) from Manhattan to get to the AirTrain. I've never made that trip personally but IMO that would be cutting it close, i.e. leaving at 4pm for a 6pm flight at JFK.
Here is the official response from the website
http://www.mta.info/mta/airtrain.htm
It takes about an hour to Jamaica from most parts in the city and about 15 min from Jamaica.